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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttagcagctacatattttaagactttaatttatatttttaactgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG

Basic information

species Zea mays
transcript GRMZM2G044011_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------------------------------------------tggttagcagctacatattttaagactttaatt---tatatttttaa----ctgaagaacacatattgcta--tatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
                                                                                            |  ||  | ||  ||| |       ||| |||   |||  ||||||     |||   ||   |   | |   | ||  || | |  |    |||  || ||||||||||||||||| |||| | ||||||||||||||||| |||||| |||||||||||||||| |||||||| || ||| ||
gtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttgagttacctcttgcggtgattgtatttgacttattagc-tatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 7
tggttagcagctacatatttt----aagactttaatttatatttttaactgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
|||||     ||     |       || |||  || ||| ||   | |      |    |||||   ||  |  || | |  |  ||| | ||     ||| || || || |  || ||  | || || ||||||||||||||| | || ||||| |||||||||||||| || ||||  
tggttgatttctgtgggtaaccacaaacactggaaattaaatacatgatcttctagttgatatttgaattaatttgtcttatttttgtctaat----aaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G36200.1 (Glycine max), 3'ss of exon 7
--tggttagcagctacatattttaagactttaatttatatttttaactgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
  |   ||   | |     | || | | | || || |  |||   |   ||        ||||| ||  |  ||   |       |||   |    |||||| || || |  || ||  | || || ||||||||||||||| | || ||||| |||||||||||||| || ||||  
attaaatacatgttcttcttgttgatagtctagttaacttttggcatgtaattgtgt-cattgcaatg-aattgatttgtcttattatgtctaataaaacagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA

upper sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------tggttagcagctacatattttaagactttaatttatat--ttttaactgaagaa-cacatattgctatatagatgg-catcctgatgtatcattttcta----------------aacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
                                                        || || |     |  || ||      ||| |  |   |  ||||  ||||| ||  |   |  |    | |||    |||||   | | |  || | ||                  |||  | |||   | ||| ||||| || |||||||| ||||||||||||||||| |||||||||||||| |||||| | 
gtactgattgcagtgacaaggtccattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattcatccaattctgttcttgtttactttattgtcttgtttggcagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|19351008|gb|BM895540.1|BM895540
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|19272449|gb|BM888705.1|BM888705
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATA-CAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|19351610|gb|BM896142.1|BM896142
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|19351009|gb|BM895541.1|BM895541
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|32825337|gb|CD965059.1|CD965059
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCGCCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|89251335|gb|DY623121.1|DY623121
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGG
EST: gi|22491504|gb|BU051427.1|BU051427
EST:     GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAG                         CATAACAGCAAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGGCAT
genomic: GTTATTCTCATGCAAGAAGGACTTGCCCACCTATTCCTCATTGGCAAAAGgtcagtggaa ... ttctaaacagCATAACAGCAA-CCCGGGCACGTATTGAAACATCAATTCCTAGGAAG-CAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
                              tcctgat  putative branch site (score: 3)
                                        tcattttct  putative PPT
                                      tatcattttctaaa  TA-rich tract